New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	3 (0.090)	10 (0.350)	7/148	1.4	84.5%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	1 (0.040)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

ATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTT  >  NZ_CP009273/4532418‑4532588                                                                                          |                                                                                  gggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCa                                                                                   >  2:6616‑M1/82‑90 (MQ=255)   gcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCaaa                                                                                 >  1:334859‑M1/80‑90 (MQ=255)    cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                                >  1:19655‑M1/79‑90 (MQ=255)    cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                                >  1:333814‑M1/79‑90 (MQ=255)    cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                                >  2:211545‑M1/79‑90 (MQ=255)    cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                                >  1:498827‑M1/79‑90 (MQ=255)      gtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTg                                                                              <  2:187081‑M1/14‑1 (MQ=255)              gtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATc                                                                      <  2:302707‑M1/22‑1 (MQ=255)                    tttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCataaat                                                                <  2:329496‑M1/28‑1 (MQ=255)                           ggTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTAc                                                         <  2:699727/90‑1 (MQ=255)                               tGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggac                                                     <  2:341632‑M1/90‑31 (MQ=255)                                 aTTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaa                                                   <  1:144847‑M1/90‑33 (MQ=255)                                                          aaaaaaCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggctt                          <  2:378172‑M1/90‑58 (MQ=255)                                                            aaaaCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaa                        <  2:663140‑M1/90‑60 (MQ=255)                                                            aaaaCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaa                        <  2:213416‑M1/90‑60 (MQ=255)                                                             ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCa                                                                          >  1:355120‑M1/22‑39 (MQ=255)                                                             ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCa                                                                          <  2:355120‑M1/18‑1 (MQ=255)                                                                cAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGAc                    <  2:359054/90‑1 (MQ=255)                                                                    taaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa                <  2:156542/90‑1 (MQ=255)                                                                    aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                                            <  1:614583‑M1/48‑1 (MQ=255)                                                                    aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                                            >  2:614583‑M1/15‑62 (MQ=255)                                                                    aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa                >  2:497002‑M1/15‑90 (MQ=255)                                                                    aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa                >  1:1785‑M1/15‑90 (MQ=255)                                                                    aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa                >  1:785013‑M1/15‑90 (MQ=255)                                                                            aGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatct        >  1:243699‑M1/1‑15 (MQ=255)                                                                            aGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaa                                                   <  2:531617‑M1/47‑33 (MQ=255)                                                                            aGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaa                                                   >  1:531617‑M1/1‑15 (MQ=255)                                                                                 aTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgtt                               <  1:248226‑M1/62‑53 (MQ=255)                                                                                 aTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgtt                               >  2:248226‑M1/1‑10 (MQ=255)                                                                                  TTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGtt  <  1:527811‑M1/90‑1 (MQ=255)                                                                                          |                                                                                  ATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTT  >  NZ_CP009273/4532418‑4532588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.